Background: In recent decades, the increase in population movements has turned the focus to imported diseases. The COVID-19 pandemic has negatively impacted the access to health care systems, especially in highly vulnerable populations. We address the effects of the pandemic on the health screening of migrant unaccompanied minors (UM) in Spain. Method: Retrospective cross-sectional study including UM screened for imported diseases with a unified protocol at a pediatric reference unit for tropical and infectious diseases in Madrid, Spain. We compared the pre-pandemic (2018–2019) and post-pandemic periods (2020–2021). Results: A total of 192 minors were screened during the study period, with a drop in UM’s referral to our center in the post-pandemic years (140 in 2018–2019 vs. 52 in 2020–2021). Out of 192, 161 (83.9%) were diagnosed with at least one medical condition. The mean age was 16.8 years (SD 0.8) and 96.9% were males. Most cases were referred for a health exam; only 38% of children were symptomatic. Eosinophilia was present in 20.8%. The most common diagnosis were latent tuberculosis infection (LTBI) (72.9%), schistosomiasis (15.1%), toxocariasis (4.9%) and strongyloidiasis (4.9%). The prevalence of LTBI did not vary significantly (69.3% vs. 82.7%, p = 0.087). A total of 38% of the patients diagnosed with LTBI never started treatment or were lost to follow-up, as were two out of three patients with active pulmonary tuberculosis. Conclusions: In this series, the number of UM referred for health screening has dropped dramatically after the COVID pandemic, and two years after the beginning of the pandemic, access to care is still limited. Lost to follow-up rates are extremely high despite institutionalization. Specific resources, including multidisciplinary teams and accessible units are needed to improve diagnoses and linkage to care in this vulnerable population.